RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780262|ref|YP_003064675.1| 30S ribosomal protein S10 [Candidatus Liberibacter asiaticus str. psy62] (104 letters) >gnl|CDD|144070 pfam00338, Ribosomal_S10, Ribosomal protein S10p/S20e. This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes. Length = 97 Score = 120 bits (303), Expect = 1e-28 Identities = 50/95 (52%), Positives = 69/95 (72%) Query: 10 ICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEM 69 I LK++D ++L+S ++ IV K+ G ++ GPIP P R TV RSPHVDKKSR+Q EM Sbjct: 3 IKLKSYDHKLLESYVKFIVEAAKRLGIKVSGPIPLPTKRLRVTVLRSPHVDKKSREQFEM 62 Query: 70 RIYKRLLYIIKPTPQTVDALMKLDIAAGVNVVIKL 104 R +KRL+ I TP+TVDAL+++D+ GV+V IKL Sbjct: 63 RTHKRLIDIYDATPETVDALLRIDLPEGVDVEIKL 97 >gnl|CDD|30400 COG0051, RpsJ, Ribosomal protein S10 [Translation, ribosomal structure and biogenesis]. Length = 104 Score = 116 bits (291), Expect = 2e-27 Identities = 57/98 (58%), Positives = 73/98 (74%) Query: 7 RICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQ 66 +I I LK+FD R+LD REIV T K++G+ + GPIP P R TV RSPH +K SR+Q Sbjct: 5 KIRIRLKSFDHRLLDQVCREIVETAKRTGADVKGPIPLPTKRERVTVLRSPHGEKDSREQ 64 Query: 67 LEMRIYKRLLYIIKPTPQTVDALMKLDIAAGVNVVIKL 104 EMR +KRL+ I+ PTP+TVDALM+LD+ AGV+V IKL Sbjct: 65 FEMRTHKRLIDIVDPTPKTVDALMRLDLPAGVDVEIKL 102 >gnl|CDD|177057 CHL00135, rps10, ribosomal protein S10; Validated. Length = 101 Score = 101 bits (254), Expect = 4e-23 Identities = 43/96 (44%), Positives = 67/96 (69%) Query: 5 NIRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSR 64 N +I I LK+F+ +L+SS ++I+ T ++ + VGPIP P R + V RSPHVDK SR Sbjct: 6 NAKIRIKLKSFNHELLNSSCKKIIDTASRTNATAVGPIPLPTKRRIYCVLRSPHVDKDSR 65 Query: 65 DQLEMRIYKRLLYIIKPTPQTVDALMKLDIAAGVNV 100 + E+R +KR++ I P+ +T+D+LMKLD+ GV++ Sbjct: 66 EHFEIRTHKRIIDIYYPSSETIDSLMKLDLPPGVDI 101 >gnl|CDD|38531 KOG3321, KOG3321, KOG3321, Mitochondrial ribosomal protein S10 [Translation, ribosomal structure and biogenesis]. Length = 175 Score = 60.8 bits (147), Expect = 9e-11 Identities = 29/84 (34%), Positives = 43/84 (51%) Query: 7 RICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQ 66 + I L+ D +LDS I T G I GP P P+ R+T+ RSP + KKS++ Sbjct: 48 LVAIELRGHDKAVLDSYTDFICRTAYYLGIPIKGPEPLPKKRERWTLLRSPFIHKKSKEN 107 Query: 67 LEMRIYKRLLYIIKPTPQTVDALM 90 E R + RL+ + T T+D + Sbjct: 108 YERRTHSRLIELYSVTGSTLDTFL 131 >gnl|CDD|36118 KOG0900, KOG0900, KOG0900, 40S ribosomal protein S20 [Translation, ribosomal structure and biogenesis]. Length = 121 Score = 52.7 bits (126), Expect = 2e-08 Identities = 26/100 (26%), Positives = 50/100 (50%), Gaps = 2/100 (2%) Query: 2 TSRNIRICICLKAFDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPH-VD 60 T +I I L + + L+ ++V K+ ++ GP+ P + + T ++P Sbjct: 16 TPEIHKIRITLTSQKVKSLEKVCADLVRGAKEKNLKVKGPVRLPTKVLKITTRKTPCGEG 75 Query: 61 KKSRDQLEMRIYKRLLYIIKPTPQTVDALMKLDIAAGVNV 100 K+ D+ EMR++KRL+ + P+ + V + + I GV V Sbjct: 76 SKTWDRFEMRVHKRLIDLHSPS-EIVKQITSISIEPGVEV 114 >gnl|CDD|144019 pfam00274, Glycolytic, Fructose-bisphosphate aldolase class-I. Length = 348 Score = 28.8 bits (65), Expect = 0.30 Identities = 12/38 (31%), Positives = 20/38 (52%) Query: 23 SMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVD 60 + R+++ TT G I G I F ++ + T + P VD Sbjct: 44 AYRQLLFTTPGLGEYISGVILFEETLYQKTDDGKPFVD 81 >gnl|CDD|31343 COG1149, COG1149, MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]. Length = 284 Score = 27.6 bits (61), Expect = 0.88 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%) Query: 21 DSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMR-IYKRL 75 + EI ++ G I+G IP+ + I VN P V+ S++ + ++L Sbjct: 225 NLGDSEIEEYCEEEGIPILGEIPYDKDIPEAYVNGEPFVEPDSKEAEAILEEAEKL 280 >gnl|CDD|146362 pfam03686, UPF0146, Uncharacterized protein family (UPF0146). The function of this family of proteins is unknown. Length = 127 Score = 27.0 bits (60), Expect = 1.2 Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 2/38 (5%) Query: 68 EMRIYK--RLLYIIKPTPQTVDALMKLDIAAGVNVVIK 103 + IY+ L+Y I+P P+ A++ + A G + IK Sbjct: 64 NISIYEGADLIYSIRPPPELQSAILDVAKAVGAPLYIK 101 >gnl|CDD|31447 COG1255, COG1255, Uncharacterized protein conserved in archaea [Function unknown]. Length = 129 Score = 26.8 bits (59), Expect = 1.5 Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 2/38 (5%) Query: 68 EMRIYK--RLLYIIKPTPQTVDALMKLDIAAGVNVVIK 103 + IY+ L+Y I+P P+ A++ + A G + IK Sbjct: 64 NISIYEGADLIYSIRPPPELQSAILDVAKAVGAPLYIK 101 >gnl|CDD|29941 cd00948, FBP_aldolase_I_a, Fructose-1,6-bisphosphate aldolase. The enzyme catalyzes the cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). This family includes proteins found in vertebrates, plants, and bacterial plant pathogens. Mutations in the aldolase genes in humans cause hemolytic anemia and hereditary fructose intolerance. The enzyme is a member of the class I aldolase family, which utilizes covalent catalysis through a Schiff base formed between a lysine residue of the enzyme and ketose substrates.. Length = 330 Score = 26.3 bits (58), Expect = 1.8 Identities = 13/36 (36%), Positives = 19/36 (52%) Query: 25 REIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVD 60 RE++ TT G I G I F ++ + T + P VD Sbjct: 48 RELLFTTPGLGQYISGVILFEETLYQKTDDGKPFVD 83 >gnl|CDD|132784 cd06874, PX_KIF16B_SNX23, The phosphoinositide binding Phox Homology domain of KIF16B kinesin or Sorting Nexin 23. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. KIF16B, also called sorting nexin 23 (SNX23), is a family-3 kinesin which harbors an N-terminal kinesin motor domain containing ATP and microtubule binding sites, a ForkHead Associated (FHA) domain, and a C-terminal PX domain. The PX domain of KIF16B binds to phosphatidylinositol-3-phosphate (PI3P) in early endosomes and plays a role in the transport of early endosomes to the plus end of microtubules. By regulating early endosome plus end motility, KIF16B modulates the balance between recycling and degradation of receptors. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Length = 127 Score = 25.8 bits (57), Expect = 2.3 Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 3/46 (6%) Query: 39 VGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIYKRLLYIIKPTPQ 84 V + FP ++ N+S V K+ R QLE + + P Sbjct: 55 VAALEFPP--KKLFGNKSERVAKERRRQLE-TYLRNFFSVCLKLPA 97 >gnl|CDD|34854 COG5257, GCD11, Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 415 Score = 25.2 bits (55), Expect = 3.6 Identities = 10/22 (45%), Positives = 14/22 (63%) Query: 81 PTPQTVDALMKLDIAAGVNVVI 102 P PQT + LM L+I N++I Sbjct: 124 PQPQTREHLMALEIIGIKNIII 145 >gnl|CDD|176674 cd07251, Glo_EDI_BRP_like_10, This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. Length = 121 Score = 25.2 bits (56), Expect = 3.6 Identities = 7/20 (35%), Positives = 12/20 (60%) Query: 82 TPQTVDALMKLDIAAGVNVV 101 + + VDA++ AAG +V Sbjct: 74 SEEEVDAVLARAAAAGATIV 93 >gnl|CDD|29575 cd02647, nuc_hydro_TvIAG, nuc_hydro_ TvIAG: Nucleoside hydrolases similar to the Inosine-adenosine-guanosine-preferring nucleoside hydrolase from Trypanosoma vivax. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. Nucleoside hydrolases vary in their substrate specificity. This group contains eukaryotic and bacterial proteins similar to the purine specific inosine-adenosine-guanosine-preferring nucleoside hydrolase (IAG-NH) from T. vivax. T. vivax IAG-NH is of the order of a thousand to ten thousand fold more specific towards the naturally occurring purine nucleosides, than towards the pyrimidine nucleosides. . Length = 312 Score = 25.3 bits (55), Expect = 3.7 Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 2/37 (5%) Query: 19 ILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNR 55 ++D + + K GS PFPRS RR Sbjct: 52 LIDRLGQRDAIPVGKGGS--RAVNPFPRSWRRDAAFS 86 >gnl|CDD|146287 pfam03568, Peptidase_C50, Peptidase family C50. Length = 339 Score = 24.6 bits (54), Expect = 5.4 Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 6/62 (9%) Query: 36 SQIVGPIPFPRSIRRFTVNRSPHVDK------KSRDQLEMRIYKRLLYIIKPTPQTVDAL 89 I+ + R + +RSP + + SRD E + II+ ++V Sbjct: 3 EIIISKDTKTLLLSRLSPDRSPIILRLPLDRHNSRDLDESTLLDEFRRIIEEDNESVTTK 62 Query: 90 MK 91 K Sbjct: 63 NK 64 >gnl|CDD|176211 cd08249, enoyl_reductase_like, enoyl_reductase_like. Member identified as possible enoyl reductase of the MDR family. 2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the alcohol dehydrogenases in this family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. Candida tropicalis enoyl thioester reductase (Etr1p) catalyzes the NADPH-dependent reduction of trans-2-enoyl thioesters in mitochondrial fatty acid synthesis. Etr1p forms homodimers with each subunit containing a nucleotide-binding Rossmann fold domain and a catalytic domain. Length = 339 Score = 24.9 bits (55), Expect = 5.8 Identities = 7/22 (31%), Positives = 10/22 (45%) Query: 24 MREIVLTTKKSGSQIVGPIPFP 45 + VLT G +V +P P Sbjct: 1 QKAAVLTGPGGGLLVVVDVPVP 22 >gnl|CDD|144549 pfam00995, Sec1, Sec1 family. Length = 558 Score = 24.5 bits (54), Expect = 6.1 Identities = 6/16 (37%), Positives = 11/16 (68%) Query: 76 LYIIKPTPQTVDALMK 91 +Y I+PT + VD ++ Sbjct: 47 IYFIRPTKENVDRIID 62 >gnl|CDD|132761 cd07076, NR_LBD_GR, Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the glucocorticoid receptor (GR): GR is a ligand-activated transcription factor belonging to the nuclear receptor superfamily. It binds with high affinity to cortisol and other glucocorticoids. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. In the absence of hormone, the glucocorticoid receptor (GR) is complexes with a variety of heat shock proteins in the cytosol. The binding of the glucocorticoids results in release of the heat shock proteins and transforms it to its active state. One mechanism of action of GR is by direct activation of gene transcription. The activated form of GR forms dimers, translocates into the nucleus, and binds to specific hormone responsive elements, activating gene transcription. GR can also function as a repressor of other gene transcription activators, such as NF-kappaB and AF-1 by directly binding to them, and bloc king the expression of their activated genes. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD also functions for dimerization and chaperone protein association. Length = 247 Score = 24.1 bits (52), Expect = 7.7 Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 7/58 (12%) Query: 15 FDSRILDSSMREIVLTTKKSGSQIVGPIPFPRSIRRFTVNRSPHVDKKSRDQLEMRIY 72 +DS + DS+ R + G Q+V + + ++I F R+ H+D DQ+ + Y Sbjct: 18 YDSSVPDSTWRIMSTLNMLGGRQVVAAVKWAKAIPGF---RNLHLD----DQMTLLQY 68 >gnl|CDD|133288 cd01888, eIF2_gamma, eIF2-gamma (gamma subunit of initiation factor 2). eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B. eIF2B is a heteropentamer, and the epsilon chain binds eIF2. Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma. It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role. eIF2-gamma is found only in eukaryotes and archaea. It is closely related to SelB, the selenocysteine-specific elongation factor from eubacteria. The translational factor components of the ternary complex, IF2 in eubacteria and eIF2 in eukaryotes are not the same protein (despite their unfortunately similar names). Both factors are GTPases; however, eubacterial IF-2 is a single polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is a member of the same family as eubacterial IF2, but the two proteins are only distantly related. This family includes translation initiation, elongation, and release factors. Length = 203 Score = 24.1 bits (53), Expect = 8.7 Identities = 8/22 (36%), Positives = 13/22 (59%) Query: 81 PTPQTVDALMKLDIAAGVNVVI 102 P PQT + L L+I +++I Sbjct: 121 PQPQTSEHLAALEIMGLKHIII 142 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.326 0.139 0.393 Gapped Lambda K H 0.267 0.0673 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,203,312 Number of extensions: 54490 Number of successful extensions: 179 Number of sequences better than 10.0: 1 Number of HSP's gapped: 178 Number of HSP's successfully gapped: 26 Length of query: 104 Length of database: 6,263,737 Length adjustment: 71 Effective length of query: 33 Effective length of database: 4,729,498 Effective search space: 156073434 Effective search space used: 156073434 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (23.5 bits)